Example 2

Bugs

See Also

Links

Methods Description

The "watershed" segmentation algorithm was used to determine the intensity values for white matter, grey matter, and CSF.
A force field was then used to fit a spherical surface to the brain. The shape of the surface fit was then evaluated against a previously derived template.
The finely grained sphere was fit to the brain.
(Segonne 2004)
"-surf" Description:
The BEM surfaces are generated after the initial mri_watershed procedure has run and produced a "brain" surface file. This brain surface file is then grown by 3mm outward to generate the "inner skull" surface. This growth is meant to account for the CSF located between the pial matter and the inner skull (see Figure 17 in Segonne et al. 2004 for a description). Next a fifth order icosahedral surface is fit arround the outer edge of the Volume and smoothed making the "outer skin" surface. Finally, this surface is shrunk by 3mm to attempt to account for the SCALP (Skin, Connective tissue, Aponeurosis, Loose areolar connective tissue, and the Pericranium). This surface is saved as the "outer skull" surface.

The -surf tool is intended as an added convenience and not as a high quality estimation of these tissue boundaries (one would not use an MPRAGE type volume for defining these tissue boundaries). For a tool designed to do that please see mri_make_bem_surfaces.